For programming:
- Python (spyder and jupyter notebook)
- R
- Fortran
- C
- Scilab
- Matlab
- NetLogo (for agent-based simulation)
For statistics and data analytics:
- JASP (with Bayesian statistics; alternative to SPSS)
- Google DataStudio
- Microsoft Excel
- Orange data mining (with Bioinformatics tools)
- Knime
- Python or R
- Cytoscape (for Network Science)
- Social Network Visualizer (alternative to Cytoscape)
- QGIS
Other software:
- Berkeley Madonna (for ODE and difference equation; for more complicated DEs, Matlab or Python can be used)
- Snoopy (for Petri nets)
- Veusz (for plotting)
- TeXstudio (for LaTex; there are also other front-end editors)
- Overleaf (for online collaborative LaTex editing)
- GeoGebra
- Zotero (for research bibliography management)
- SageMath
